Variant report

Variant	rs6673580
Chromosome Location	chr1:10020894-10020895
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10009468..10012009-chr1:10018654..10021337,2	MCF-7	breast:
2	chr1:9968056..9971039-chr1:10018958..10022091,3	K562	blood:
3	chr1:10001983..10003489-chr1:10020607..10022656,2	K562	blood:

Variant related genes	Relation type
ENSG00000162441	Chromatin interaction
ENSG00000173614	Chromatin interaction
ENSG00000178585	Chromatin interaction
ENSG00000228150	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10779735	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11121508	0.93[AFR][1000 genomes]
rs12026401	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128632	0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12128636	0.87[AFR][1000 genomes]
rs1220398	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1220422	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1237370	0.93[AFR][1000 genomes]
rs12744387	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2380188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3013785	0.87[AFR][1000 genomes]
rs4073852	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41280780	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782860	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61785621	0.95[AFR][1000 genomes]
rs6541074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663108	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6683452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72859517	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522568	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943169	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv1005461	chr1:9972921-10038862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	nsv534855	chr1:9972921-10038862	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6673580	LZIC	cis	Lymphoblastoid	GTEx
rs6673580	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10004000-10034000	Weak transcription	Aorta	Aorta
2	chr1:10004200-10021000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:10004200-10033800	Weak transcription	Gastric	stomach
4	chr1:10004400-10021200	Weak transcription	HSMM	muscle
5	chr1:10004400-10031600	Weak transcription	Fetal Intestine Large	intestine
6	chr1:10004600-10021000	Weak transcription	HSMMtube	muscle
7	chr1:10004600-10032400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:10004800-10031600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:10004800-10032200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:10004800-10032400	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:10008000-10031800	Weak transcription	Lung	lung
12	chr1:10008000-10032000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:10008000-10032200	Weak transcription	Colonic Mucosa	Colon
14	chr1:10008000-10035000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:10008200-10032000	Weak transcription	Liver	Liver
16	chr1:10008200-10032200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:10008400-10031800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:10008400-10032000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:10008400-10032200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:10008600-10031800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:10008600-10033200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:10008600-10035600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:10010800-10023000	Weak transcription	HepG2	liver
24	chr1:10010800-10032000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:10010800-10032000	Weak transcription	Thymus	Thymus
26	chr1:10010800-10032200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:10010800-10032600	Weak transcription	Primary T cells from cord blood	blood
28	chr1:10010800-10034800	Weak transcription	NHEK	skin
29	chr1:10010800-10035000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:10010800-10035600	Weak transcription	Fetal Kidney	kidney
31	chr1:10010800-10036400	Weak transcription	Esophagus	oesophagus
32	chr1:10011000-10021000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:10011000-10021000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:10011000-10021600	Weak transcription	Brain Angular Gyrus	brain
35	chr1:10011000-10031800	Weak transcription	Left Ventricle	heart
36	chr1:10011000-10031800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:10011000-10032200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:10011000-10032200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:10011000-10032400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:10011000-10032600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:10011000-10032600	Weak transcription	Fetal Thymus	thymus
42	chr1:10011000-10034200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:10011000-10044800	Weak transcription	NHDF-Ad	bronchial
44	chr1:10011200-10031600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:10011200-10032200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:10011200-10032400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:10011400-10021200	Weak transcription	Hela-S3	cervix
48	chr1:10011400-10027800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:10011400-10032000	Weak transcription	Adipose Nuclei	Adipose
50	chr1:10011400-10032600	Weak transcription	Brain Hippocampus Middle	brain

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